error with official code

[jwchen25]

conda env:

conda create -n py38 python=3.8
conda activate py38
conda install rdkit openbabel xtb-python qcengine spyrmsd morfeus-ml -c conda-forge

code from official ducument:

from morfeus.conformer import ConformerEnsemble

ce = ConformerEnsemble.from_rdkit("CCCC", optimize="MMFF94")
ce.prune_rmsd()
ce.sort()
ce.get_relative_energies()

# Optimize with GFN-FF
model={"method": "GFN-FF"}
ce.optimize_qc_engine(program="xtb", model=model)
ce.get_relative_energies()

# Do single points with GFN2-xTB
model={"method": "GFN2-xTB"}
ce.sp_qc_engine(program="xtb", model=model)
ce.get_relative_energies()

error:
Traceback (most recent call last):
File "/home/jwchen/work/code/PassivatorML/descriptors/morfeus/test.py", line 10, in
ce.optimize_qc_engine(program="xtb", model=model)
File "/home/jwchen/software/anaconda3/envs/py38/lib/python3.8/site-packages/morfeus/conformer.py", line 861, in optimize_qc_engine
opt_coordinates, energies = optimize_qc_engine(
File "/home/jwchen/software/anaconda3/envs/py38/lib/python3.8/site-packages/morfeus/qc.py", line 98, in optimize_qc_engine
raise Exception(opt.error.error_message)
Exception: QCEngine Resource Error: Procedure berny is registered with QCEngine, but cannot be found.

[kjelljorner]

Try installing pyberny

pip install pyberny

[jwchen25]

thank you very much, it works

[jwchen25]

Geometry Optimization of QCEngine:

for optimize_qc_engine(procedure="geometric"), it needs:
geomeTRIC
pip install geometric

for optimize_qc_engine(procedure="berny"), it needs:
Pyberny
pip install pyberny

[kjelljorner]

Yes, they are further dependencies of QCEngine, but it might be good to list them in the morfeus documentation as well. Which of these sections do you think would be best from a user perspective:

• https://kjelljorner.github.io/morfeus/installation.html
• https://kjelljorner.github.io/morfeus/conformer.html#optimization-and-ranking

[jwchen25]

I think https://kjelljorner.github.io/morfeus/conformer.html#optimization-and-ranking is better, people who need to optimized molecules will read it and then install further dependencies of QCEngine.

It would be great if you could provide a conda virtual environment configuration file (.yml/.yaml) for a fully functional version of the morfeus software.

[kjelljorner]

That's a good idea, there are already some .yml files available for optional dependencies, but I should probably add geometric and pyberny to those

[kjelljorner]

Docs updated at https://kjelljorner.github.io/morfeus/conformer.html#optimization-and-ranking and pyberny and geometric added to the yml file https://github.com/kjelljorner/morfeus/blob/main/environment-opt.yml

[kjelljorner]

Thanks for the feedback